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On the importance of ribose orientation in the substrate activation of coenzyme B12-dependent mutases
University of Sydney, Australia and Uppsala University, Sweden.
University of Sydney, Australia.
University of Sydney, Australia.
Rudjer Boskovic Institute, Zagreb, Croatia.
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2009 (English)In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 15, no 34, 8578-8585 p.Article in journal (Refereed) Published
Abstract [en]

The degree to which the corrin ring portion of coenzyme B12 can facilitate the H-atom-abstraction step in the glutamate mutase (GM)-catalyzed reaction of (S)-glutamate has been investigated with density functional theory. The crystal structure of GM identifies two possible orientations of the ribose portion of coenzyme B12. In one orientation (A), the OH groups of the ribose extend away from the corrin ring, whereas in the other orientation (B) the OH groups, especially that involving O3’, are instead directed towards the corrin ring. Our calculations identify a sizable stabilization amounting to about 30 kJ mol–1 in the transition structure (TS) complex corresponding to orientation B (TSBCorIm). In the TS complex where the ribose instead is positioned in orientation A, no such effect is manifested. The observed stabilization in TSBCorIm appears to be the result of favorable interactions involving O3’ and the corrin ring, including a C–H···O hydrogen bond. We find that the degree of stabilization is not particularly sensitive to the Co–C distance. Our calculations show that any potential stabilization afforded to the H-atom abstraction step by coenzyme B12 is sensitive to the orientation of the ribose moiety.

Place, publisher, year, edition, pages
John Wiley & Sons, 2009. Vol. 15, no 34, 8578-8585 p.
Keyword [en]
density functional calculations; enzymes; molecular modeling; radicals; reaction mechanisms
National Category
Natural Sciences
URN: urn:nbn:se:liu:diva-96737DOI: 10.1002/chem.200901002OAI: diva2:643067
Available from: 2013-08-26 Created: 2013-08-26 Last updated: 2013-09-02Bibliographically approved

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Durbeej, Bo
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